Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
What is the ruling on undoing braids of hair during the ritual bath?
It is not a condition to undo braids if the water reaches all the hair and penetrates to its base. If the water does not reach except by undoing the braids, then it is obligatory to undo them for the water to reach. And Allah the Almighty knows best.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
What should a person who was favored from Allah with a newborn, but couldn`t afford an Aqeeqah, do?
Aqeeqah (the sheep slaughtered on the seventh day from the child`s birth) is a desirable Sunnah for the financially able since Allah, The Exalted, charges not a soul beyond its capacity. Therefore, if the father couldn`t afford the Aqeeqah before the end of his wife`s confinement, then it isn`t due on him, and if he was able to afford it later on, then it is permissible, but if he didn`t until the child reached puberty, the latter can offer the Aqeeqah himself.